improve sdrf validation hint

.github/workflows/ci.yml

@@ -56,14 +56,14 @@ jobs:
           mamba-version: "*"
           channels: conda-forge,defaults
 
-      #- name: Install micromamba as mamba
-      #  if: matrix.exec_profile == 'conda'
-      #  run: |
-      #    wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
-      #    mv bin/micromamba bin/mamba
-      #    echo "$(pwd)/bin" >> $GITHUB_PATH
-      #    echo "$(pwd)/mamba/bin" >> $GITHUB_PATH
-      #    ./bin/mamba shell init -s bash -p ./mamba
+      # - name: Install micromamba as mamba
+      #   if: matrix.exec_profile == 'conda'
+      #   run: |
+      #     wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+      #     mv bin/micromamba bin/mamba
+      #     echo "$(pwd)/bin" >> $GITHUB_PATH
+      #     echo "$(pwd)/mamba/bin" >> $GITHUB_PATH
+      #     ./bin/mamba shell init -s bash -p ./mamba
 
       - name: Run pipeline with test data
         if: matrix.exec_profile != 'conda'

bin/check_samplesheet.py

@@ -49,7 +49,13 @@ def check_sdrf(check_ms, sdrf):
     errors = df.validate(DEFAULT_TEMPLATE)
     if check_ms:
         errors = errors + df.validate(MASS_SPECTROMETRY)
-    print(errors)
+    for error in errors:
+        print(error)
+    if not errors:
+        print("Everying seems to be fine. Well done.")
+    else:
+        print("There were validation errors!")
+    sys.exit(bool(errors))
 
 
 def check_expdesign(expdesign):

subworkflows/local/id.nf

@@ -40,10 +40,12 @@ workflow ID {
     // SUBWORKFLOW: PSMFDRCONTROL
     //
     ch_psmfdrcontrol = Channel.empty()
+    ch_consensus_results = Channel.empty()
     if (params.search_engines.split(",").size() > 1) {
         CONSENSUSID(PSMRESCORING.out.results.groupTuple(size: params.search_engines.split(",").size()))
         ch_software_versions = ch_software_versions.mix(CONSENSUSID.out.version.ifEmpty(null))
         ch_psmfdrcontrol = CONSENSUSID.out.consensusids
+        ch_consensus_results = CONSENSUSID.out.consensusids
     } else {
         ch_psmfdrcontrol = PSMRESCORING.out.results
     }
@@ -65,5 +67,6 @@ workflow ID {
     emit:
     id_results              = ch_id_results
     psmrescoring_results    = PSMRESCORING.out.results
+    ch_consensus_results    = ch_consensus_results
     version                 = ch_software_versions
 }

workflows/lfq.nf

@@ -71,12 +71,17 @@ workflow LFQ {
         .map { it -> it[1] }
         .set { ch_pmultiqc_ids }
 
+    ID.out.ch_consensus_results
+        .map { it -> it[1] }
+        .set { ch_pmultiqc_consensus }
+
     emit:
-    ch_pmultiqc_ids = ch_pmultiqc_ids
-    final_result    = PROTEOMICSLFQ.out.out_mztab
-    versions        = ch_software_versions
-    msstats_in      = PROTEOMICSLFQ.out.out_msstats
-    msstats_out     = ch_msstats_out
+    ch_pmultiqc_ids         = ch_pmultiqc_ids
+    ch_pmultiqc_consensus   = ch_pmultiqc_consensus
+    final_result            = PROTEOMICSLFQ.out.out_mztab
+    versions                = ch_software_versions
+    msstats_in              = PROTEOMICSLFQ.out.out_msstats
+    msstats_out             = ch_msstats_out
 }
 
 /*

workflows/quantms.nf

@@ -117,6 +117,7 @@ workflow QUANTMS {
     ch_pipeline_results = Channel.empty()
     ch_ids_pmultiqc = Channel.empty()
     ch_msstats_in = Channel.empty()
+    ch_consensus_pmultiqc = Channel.empty()
 
     //
     // MODULE: Generate decoy database
@@ -141,12 +142,14 @@ workflow QUANTMS {
 
     TMT(ch_fileprep_result.iso, CREATE_INPUT_CHANNEL.out.ch_expdesign, ch_searchengine_in_db)
     ch_ids_pmultiqc = ch_ids_pmultiqc.mix(TMT.out.ch_pmultiqc_ids)
+    ch_consensus_pmultiqc = ch_consensus_pmultiqc.mix(TMT.out.ch_pmultiqc_consensus)
     ch_pipeline_results = ch_pipeline_results.mix(TMT.out.final_result)
     ch_msstats_in = ch_msstats_in.mix(TMT.out.msstats_in)
     ch_versions = ch_versions.mix(TMT.out.versions.ifEmpty(null))
 
     LFQ(ch_fileprep_result.lfq, CREATE_INPUT_CHANNEL.out.ch_expdesign, ch_searchengine_in_db)
     ch_ids_pmultiqc = ch_ids_pmultiqc.mix(LFQ.out.ch_pmultiqc_ids)
+    ch_consensus_pmultiqc = ch_consensus_pmultiqc.mix(LFQ.out.ch_pmultiqc_consensus)
     ch_pipeline_results = ch_pipeline_results.mix(LFQ.out.final_result)
     ch_msstats_in = ch_msstats_in.mix(LFQ.out.msstats_in)
     ch_versions = ch_versions.mix(LFQ.out.versions.ifEmpty(null))
@@ -184,7 +187,8 @@ workflow QUANTMS {
     SUMMARYPIPELINE (
         CREATE_INPUT_CHANNEL.out.ch_expdesign
             .combine(ch_pipeline_results.ifEmpty([]).combine(ch_multiqc_files.collect())
-            .combine(ch_ids_pmultiqc.collect().ifEmpty([])))
+            .combine(ch_ids_pmultiqc.collect().ifEmpty([]))
+            .combine(ch_consensus_pmultiqc.collect().ifEmpty([])))
             .combine(ch_msstats_in.ifEmpty([])),
         ch_multiqc_quantms_logo
     )

workflows/tmt.nf

@@ -79,10 +79,15 @@ workflow TMT {
         .map { it -> it[1] }
         .set { ch_pmultiqc_ids }
 
+    ID.out.ch_consensus_results
+        .map { it -> it[1] }
+        .set { ch_pmultiqc_consensus }
+
     emit:
-    ch_pmultiqc_ids = ch_pmultiqc_ids
-    final_result    = PROTEINQUANT.out.out_mztab
-    msstats_in  = PROTEINQUANT.out.msstats_csv
-    msstats_out     = ch_msstats_out
-    versions        = ch_software_versions
+    ch_pmultiqc_ids         = ch_pmultiqc_ids
+    ch_pmultiqc_consensus   = ch_pmultiqc_consensus
+    final_result            = PROTEINQUANT.out.out_mztab
+    msstats_in              = PROTEINQUANT.out.msstats_csv
+    msstats_out             = ch_msstats_out
+    versions                = ch_software_versions
 }